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Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation

ABSTRACT: To assess variation and inheritance of genome-wide patterns of DNA methylation simultaneously in humans, we applied reduced representation bisulfite sequencing (RRBS) to somatic DNA from six members of a three-generation family.

ORGANISM(S): Homo sapiens

PROVIDER: GSE30253 | GEO | 2011/07/01

SECONDARY ACCESSION(S): PRJNA143745

REPOSITORIES: GEO

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Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation

Project description:To assess variation and inheritance of genome-wide patterns of DNA methylation simultaneously in humans, we applied reduced representation bisulfite sequencing (RRBS) to somatic DNA from six members of a three-generation family. Reduced representation bisulfite sequencing was applied to genomic DNA from leukocytes of 6 family members and two unrelated individuals.

2011-07-01 | E-GEOD-30253 | biostudies-arrayexpress

Project description:This study investigates differences in DNA methylation that are associated with chronic cociane dependence in post-mortem dorsolateral caudate tissue samples from human brain. The data were generated with reduced representation bisulfite sequencing (RRBS) and compared to data generated in caudate tissue from psychiatrically healthy controls.

2021-09-11 | GSE137364 | GEO

Assessing the influence of DNMTi on human CD8+ T cells on a global level using methylome and transcriptome analyses.

Project description:RRBS (Reduced Representation Bisulfite Sequencing) and RNA-seq were performed on human CD8+ T cells from peripheral blood of three independent healthy donors to study the influence of DNMTi on CD8+ T cells on a global level.

2021-02-08 | GSE93383 | GEO

Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

Project description:DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging due to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of CpG Islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared to adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development. Laser capture microdissection-reduced representation bisulfite sequencing and reduced representation bisulfite sequencing on human blood leukocyte, human endometrial tumor, mouse liver tissue, and mouse normal and neoplastic adrenal tissue

2013-03-21 | E-GEOD-45361 | biostudies-arrayexpress

Genome-wide DNA methylation analysis for cartilage tissues

Project description:We performed reduced representation bisulfite sequencing (RRBS) for cartilage tissues to compare sex differences of DNA methylation status of X chromosomes including the pseudoautosomal region.

2024-04-10 | GSE188375 | GEO

Genome-wide DNA methylation profiling of human dorsolateral prefrontal cortex

Project description:Reduced representation bisulfite sequencing (RRBS) was conducted on dorsolateral prefrontal cortex tissue samples taken from the brains of control individuals not affected by neurological disorder DNA methylation profiling was conducted using RRBS and the Illumina Genome Analyzer IIx

2012-11-29 | E-GEOD-42590 | biostudies-arrayexpress

Genome-scale DNA methylation maps of mouse chromaffin cells with or without Sdhb knock-out.

Project description:We report the analysis of DNA methylation in mouse chromaffin cell lines using reduced representation bisulfite sequencing (RRBS). We compared DNA methylation profiles of cell lines with or without a knock-out of Sdhb gene, showing that Sdhb disruption results in a hypermethylator phenotype. Reduced representation bisulfite sequencing of 4 mouse chromaffin cell samples (2 Sdhb wild-type and 2 Sdhb knock-out).

2013-05-06 | E-GEOD-44350 | biostudies-arrayexpress

Smad4 restricts injury-provoked biliary proliferation and carcinogenesis (AKPS_EV_vs_Smad4_MethylSeq)

Project description:Reduced representation bisulfite sequencing (RRBS) on the same TGFβ-treated AKPS lines (with EV or Smad4) revealed that Smad4 impacts DNA methylation (DNAme), with decreases in intergenic DNAme as the most impacted in our CCA models.

2023-12-07 | GSE237680 | GEO

Methylation profile generated by reduced representation bisulfite sequencing (RRBS) of H2O2-treated and untreated HCT116 cells

Project description:DNA methylation is an important regulatory mechanism that contributes to transcriptional repression. To examine whether DNA methylation affects the transcriptional changes of DNA repair genes under H2O2-induced oxidative stress, we performed reduced representation bisulfite sequencing (RRBS) in H2O2-treated and untreated HCT116 cells.

2016-05-01 | GSE75963 | GEO

Genome-wide DNA methylation map of Zebrafish liver

Project description:Using a pooled (n=10) zebrafish liver DNA, we generated base-resolution DNA methylation maps to document epigenetic landscape in zebrafish genome. Here we generated single-nucleotide resoultion DNA methylation map of zebrafish pooled liver sample using Reduced Representation Bisulfite Sequencing (RRBS)

2014-10-01 | E-GEOD-59917 | biostudies-arrayexpress

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